Package index • metasalmon

Dictionary Functions

Infer, validate, and apply semantic data dictionaries

infer_dictionary(): Infer a starter dictionary from a data frame
validate_dictionary(): Validate a salmon data dictionary
apply_salmon_dictionary(): Apply a salmon dictionary to a data frame

Package Functions

Create and read Salmon Data Packages

create_salmon_datapackage(): Create a Salmon Data Package
read_salmon_datapackage(): Read a Salmon Data Package

Semantic Helpers

Semantic suggestion and vocabulary search capabilities

suggest_semantics(): Suggest semantic annotations for a dictionary
find_terms(): Find candidate terms across external vocabularies
sources_for_role(): Get recommended sources for a given role
deduplicate_proposed_terms(): Deduplicate proposed ontology terms

Ontology + Validation

Fetch the ontology and validate semantic coverage

fetch_salmon_ontology(): Fetch the DFO Salmon Ontology with caching
validate_semantics(): Validate semantics with graceful gap reporting
suggest_facet_schemes(): Suggest facet schemes for proposed terms

Darwin Core (DwC-DP)

Darwin Core Data Package mapping and export helpers

suggest_dwc_mappings(): Suggest Darwin Core Data Package mappings for dictionary columns
dwc_dp_build_descriptor(): Build a DwC-DP datapackage descriptor (export helper)

GitHub Access

Authenticate once and read CSVs from private GitHub repositories

ms_setup_github(): Set up GitHub access for private repositories
github_raw_url(): Build a stable raw GitHub URL
read_github_csv(): Read a CSV from a GitHub repository
read_github_csv_dir(): Read all CSV files from a GitHub directory

ICES Vocabulary

Access ICES reference codes and vocabulary

ices_vocab: ICES controlled vocabularies (code lists)
ices_code_types(): List ICES code types
ices_codes(): List ICES codes for a code type
ices_find_code_types(): Find ICES code types by text match
ices_find_codes(): Find ICES codes within a code type by text match